Links to official web pages:

Research:

We are interested in the structure, function,
and design of protein-DNA complexes, focusing on the 50-1000 bp length
scale. This is the biologically-relevant domain of
multi-protein DNA complexes, DNA looping, chromatin, and DNA topology. We
study the shapes of protein-nucleic acid complexes and DNA loops, the functional
consequences of changes in shape,
and the design and control of DNA and protein-DNA shape. We use molecular
biology techniques like DNA ring closure, electrophoretic mobility shift
assays, and footprinting to guide hypotheses, and then move on to characterization
with fluorescence resonance energy transfer (FRET), single-molecule FRET,
and atomic force microscopy (AFM). Accomplishments in this area include
the identification of negatively supercoiled minicircles upon ring closure
of short fragments bound by the TATA box binding protein (TBP), which led
to a proposal on the coupling between chromatin remodeling during transcriptional
activation and enhanced TBP binding. We also showed that DNA loops anchored
by the Lac repressor can exist in at least two conformations that are distinguishable
by bulk and single-molecule FRET. This has recently been expanded to include a systematic looping landscape that should provide valuable constraints for systems biology models of transcriptional regulation. Functional studies of gene regulation
in bacteria complement our in vitro work. We have recently designed the world's smallest and stiffest DNA looping proteins, based on a coiled coil motif. Currently we are excited
about designing DNA and proteins to form self-assembled protein-DNA nanostructures.
Finally, we have applied interests in the hybridization thermodynamics
of oligonucleotides containing modified chemistries, with an eye to improving
the use of nucleic acids in diagnostics and therapeutics.

Teaching:

I teach several general chemistry, biochemistry, and special interest
courses. Here is a collection of general teaching
resources, including figures created for several courses, and instructions,
examples, and tutorials for Jmol/Rasmol/Pymol-based viewing of biomolecule
PDB files.
For recent courses, lecture notes and other resources are available mainly
through the ELMS system.

Current Teaching:

Chemistry 271, General Chemistry and Energetics:
Syllabus.This is a course
covering the traditional material for the second half of general chemistry,
but given in the fourth semester of the undergraduate series, after organic
chemistry instead of before. I also include special topics applications like DNA hybridization
thermodynamics and the redox reactions driving anaerobic metabolism.

I occasionally teach a graduate biochemistry elective (BCHM 673) on regulatory networks, which most recently included modules on bacterial chemotaxis, gene regulation by nuclear hormone receptors and connections to Hsp90, G proteins and GPCRs, signal transduction in diabetes, and the principles of regulatory networks a la Alon.

At various times I have taught Biochem 461 (Biomolecules and Enzymes), 463 (Biochemistry and Physiology), 465 (Biological Information Processing), and parts of 462 (Metabolism).